crossing96/oncoscreening huggingface dataset:
Increased CD4(+) T cell lineage commitment determined by CpG methylation correlates with better prognosis in urinary bladder cancer patients.	BACKGROUND: Urinary bladder cancer is a common malignancy worldwide. Environmental factors and chronic inflammation are correlated with the disease risk. Diagnosis is performed by transurethral resection of the bladder, and patients with muscle invasive disease preferably proceed to radical cystectomy, with or without neoadjuvant chemotherapy. The anti-tumour immune responses, known to be initiated in the tumour and draining lymph nodes, may play a major role in future treatment strategies. Thus, increasing the knowledge of tumour-associated immunological processes is important. Activated CD4(+) T cells differentiate into four main separate lineages: Th1, Th2, Th17 and Treg, and they are recognized by their effector molecules IFN-γ, IL-13, IL-17A, and the transcription factor Foxp3, respectively. We have previously demonstrated signature CpG sites predictive for lineage commitment of these four major CD4(+) T cell lineages. Here, we investigate the lineage commitment specifically in tumour, lymph nodes and blood and relate them to the disease stage and response to neoadjuvant chemotherapy. RESULTS: Blood, tumour and regional lymph nodes were obtained from patients at time of transurethral resection of the bladder and at radical cystectomy. Tumour-infiltrating CD4(+) lymphocytes were significantly hypomethylated in all four investigated lineage loci compared to CD4(+) lymphocytes in lymph nodes and blood (lymph nodes vs tumour-infiltrating lymphocytes: IFNG -4229 bp p < 0.0001, IL13 -11 bp p < 0.05, IL17A -122 bp p < 0.01 and FOXP3 -77 bp p > 0.05). Examination of individual lymph nodes displayed different methylation signatures, suggesting possible correlation with future survival. More advanced post-cystectomy tumour stages correlated significantly with increased methylation at the IFNG -4229 bp locus. Patients with complete response to neoadjuvant chemotherapy displayed significant hypomethylation in CD4(+) T cells for all four investigated loci, most prominently in IFNG p < 0.0001. Neoadjuvant chemotherapy seemed to result in a relocation of Th1-committed CD4(+) T cells from blood, presumably to the tumour, indicated by shifts in the methylation patterns, whereas no such shifts were seen for lineages corresponding to IL13, IL17A and FOXP3. CONCLUSION: Increased lineage commitment in CD4(+) T cells, as determined by demethylation in predictive CpG sites, is associated with lower post-cystectomy tumour stage, complete response to neoadjuvant chemotherapy and overall better outcome, suggesting epigenetic profiling of CD4(+) T cell lineages as a useful readout for clinical staging.	bladder
Improved outcomes with pembrolizumab treatment in two cases of double cancer including non-small-cell lung cancer.	Lung cancer is a major health concern worldwide, but new immunotherapeutic treatments for lung cancer have shown great promise and the prognosis for many severe cancers including lung cancer has been improving. In May 2017, the Food and Drug Administration approved pembrolizumab, a therapeutic antibody that blocks lymphocytic programmed death-1 (PD-1), as a first-line treatment for any solid tumor with specific genetic features. Pembrolizumab is a therapeutic antibody that blocks lymphocytic PD-1, the ligand of which (PD-L1) is expressed on tumor cells and which can prevent the immune system from recognizing and destroying tumors. Here, we report two cases of double cancer (case 1: lung and bladder cancer; case 2: gastric and lung cancer) in which pembrolizumab was effective for the treatment of both cancers in each patient.	bladder
(11)C-acetate PET/MRI in bladder cancer staging and treatment response evaluation to neoadjuvant chemotherapy: a prospective multicenter study (ACEBIB trial).	BACKGROUND: To evaluate the accuracy of (11)C-acetate Positron Emission Tomography/Magnetic Resonance Imaging (PET/MRI) in bladder cancer (BC) staging and monitoring response to neoadjuvant chemotherapy (NAC). METHODS: Eighteen patients were prospectively enrolled. Fifteen treatment naive patients underwent (11)C-acetate PET/MRI before transurethral resection of bladder tumor (TUR-BT) for primary tumor evaluation. Five patients with muscle invasive BC were imaged after NAC and prior to radical cystectomy (RC) with extended pelvic lymph node dissection (ePLND) for NAC treatment response evaluation. Two patients were part of both cohorts. (11)C-acetate PET/MRI findings were correlated with histopathology. Accuracy for lymph node detection was evaluated on patient and the ePLND template (10 regions) levels. RESULTS: The sensitivity, specificity and accuracy of (11)C-acetate PET/MRI for the detection of muscle invasive BC was 1.00, 0.69 and 0.73 while the area under the receiver operating characteristic curve (95% confidence interval) was 0.85 (0.55-1.0), respectively. All five NAC patients underwent chemotherapy as planned and (11)C-acetate PET/MRI correctly staged three patients, overstaged one and understaged one patient compared with RC and ePLND findings. A total of 175 lymph node were removed, median of 35 (range, 27-43) per patient in five patients who had RC and ePLND while 12 (7%) harboured metastases. Sensitivity, specificity, accuracy and AUC for N-staging were 0.20, 0.96, 0.80 and 0.58 on the ePLND template (10 regions) level. CONCLUSIONS: (11)C-acetate PET/MRI is feasible for staging of BC although sensitivity for the detection of nodal metastases is low. Monitoring response to NAC shows promise and warrants evaluation in larger studies. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01918592 , registered August 8 2013.	bladder
Collagen Type VI Alpha 3 Chain Promotes Epithelial-Mesenchymal Transition in Bladder Cancer Cells via Transforming Growth Factor β (TGF-β)/Smad Pathway.	BACKGROUND Collagen type VI alpha 3 chain (COL6A3) has been proven to be a biomarker in the occurrence and development of bladder cancer, which is the most common malignant tumor in the urinary system. This study aimed to explore the effect and molecular mechanism of COL6A3 on EMT in vitro induced by TGF-β/Smad in bladder carcinoma. MATERIAL AND METHODS There were 42 patients included in the Kaplan-Meier survival analysis. A cell counting kit-8 (CCK-8) assay and an angiogenesis assay were used to measure cell proliferation and tube formation, respectively. Western blot analysis and quantitative reverse transcription-polymerase chain reaction (qPCR) were conducted for the proteins and mRNAs expression. RESULTS COL6A3 was highly expressed in tissues and cells of bladder cancer. COL6A3 silencing could inhibit the cell proliferation and angiopoiesis. In addition, COL6A3 silencing obviously suppressed the levels of matrix metalloproteinase-2 (MMP2), Matrix metalloproteinase-9 (MMP9), and vimentin. On the contrary, the levels of epithelium-specific cell-cell adhesion molecule (E-cadherin) and tumor inhibitor of metalloproteinase-1 (TIMP-1) were significantly increased. Furthermore, we found that COL6A3 silencing reduced the activity of p-Smad2, p-Smad3, and transforming growth factor β (TGF-β). CONCLUSIONS COL6A3 could influence the viability and angiogenesis of bladder cancer cells. COL6A3 may have a certain relationship with the TGF-β/Smad-induced EMT process.	bladder
[A Case of Metachronous Cancer Originating from Five Different Organs].	Advances and improvements in the early detection, diagnosis, and treatment modalities have increased the opportunities to treat multiple primary malignancies. Herein, we report a male patient with five metachronous cancers. The patient had initially undergone partial tongue resection for tongue cancer in 2003 at the age of 57 years and was subsequently diagnosed with acute promyelocytic leukemia, duodenal cancer, prostate cancer, and bladder cancer, over a period of 13 years. The patient underwent androgen deprivation therapy and palliative radiation therapy for the management of metastatic prostate cancer in 2016. The poor prognosis of the patient was thought to be related to be the prostate cancer because the other cancers were either in remission or localized. The occurrence of five metachronous cancers is extremely rare, and this is the fourth case to be reported in the Japanese literature.	bladder
Indication for a Single Postoperative Instillation of Chemotherapy in Non-muscle-invasive Bladder Cancer: What Factors Should Be Considered?	An early single instillation of intravesical chemotherapy (SICI) used immediately after transurethral resection of the bladder (TURB) can significantly reduce the recurrence rate in selected patients with non-muscle-invasive bladder cancer (NMIBC). SICI should be used in patients with low-risk and with selected intermediate-risk tumours, in particular for multiple primary small papillary tumours, single primary papillary tumours >3cm, and single recurrent papillary tumours recurring >1yr after the previous resection. The available data do not support any recommendation to reduce the role of SICI in patients after fluorescence cystoscopy-guided TURB or en bloc TURB. SICI can even provide some benefit in patients with intermediate-risk tumours subsequently treated with further instillations. During instillation, contraindications should be taken into account and safety measures should be applied. PATIENT SUMMARY: An early single instillation of intravesical chemotherapy immediately after transurethral resection of the bladder can significantly reduce the recurrence rate in selected patients with non-muscle-invasive bladder cancer. It should be used in patients with low-risk and selected intermediate-risk tumours.	bladder
Defining the frequency of human papillomavirus and polyomavirus infection in urothelial bladder tumours.	Given the contradictory nature of the literature regarding the role of human papillomaviruses and polyomaviruses in the pathogenesis of urothelial bladder cancer (UBC), we sought to investigate the frequency of their involvement in a large cohort of primary UBCs. DNA was extracted from 689 fresh-frozen UBC tissues and screened for the presence of high-risk human papillomavirus (HPV) types 16 and 18 and BKV/JCV genomic DNA by qPCR. In positive cases, viral identity was confirmed by Sanger sequencing and viral gene expression was analysed by RT-PCR or immunohistochemistry. All 689 UBCs were negative for HPV18. One UBC from a female patient with areas of squamous differentiation was positive for HPV16. The qPCR data indicated variable levels of polyomavirus in 49 UBCs. In the UBCs with low C(t)s we were able to confirm that 23 were BKV and 6 were JCV by Sanger sequencing. Polyomavirus large T antigen expression was low but detectable in 70% of the sequencing-confirmed polyomavirus positive samples. Thus, in United Kingdom patients, the presence of HPV DNA sequences is extremely rare in UBC (<1% of cases). Polyomavirus DNA (predominantly BKV) is more common in UBC, but still only detectable in 7% of cases and in many of these cases at low copy number. We have performed the largest virus screening to date in UBC, finding that HPV16, HPV18 and HPyV are unlikely to be common causative agents in UBC.	bladder
[Small cell neuroendocrine carcinoma of the bladder: Report of five cases and a review of the literature].	Neuroendocrine small cell carcinoma of the bladder is a rare and aggressive tumour, accounting for less than 1% of all bladder tumours. Given its rarity and the absence of randomized trials, the therapeutic management of these tumours remains difficult. By analogy with small cell lung cancer, multimodal treatment is often proposed. Radical cystectomy plus chemotherapy and chemoradiation therapy are associated with better survival compared to monotherapy. We report our experience in the management of these tumours with literature review.	bladder
Prognostic Signature of Alternative Splicing Events in Bladder Urothelial Carcinoma Based on Spliceseq Data from 317 Cases.	"BACKGROUND/AIMS: Increasing evidences indicated the important roles of alternative splicing in the progression and prognosis of bladder urothelial carcinoma (BLCA). However, most previous research has focused on one or several alternative splicing events, without a comprehensive evaluation of the prognostic value of splicing events in BLCA. In this study, we aimed to determine risk scores for predicting prognosis of BLCA patients based on splicing events. METHODS: RNA-sequencing data and clinical information of BLCA patients were downloaded from The Cancer Genome Atlas, and data of splicing events were obtained from the SpliceSeq database. Univariate and multivariate Cox regression analyses were employed to identify survival-associated alternative spicing events (SASEs) and to calculate risk scores. Protein-protein interaction analysis of genes of the SASEs was performed using STRING, a database of known and predicted protein-protein interactions, and pathway enrichment analysis of the genes was implemented using the Database for Annotation, Visualization and Integrated Discovery (version 6.8). Receiver operating characteristic (ROC) curves and Kaplan-Meier analysis were used to evaluate the clinical significance of genes from the SASEs for building a risk score in BLCA. Correlation between splicing events of splicing factors and non-splicing factors were analyzed with Pearson correlation coefficient. A potential regulatory network was then built using Cytoscape 3.5. RESULTS: In total, 39,508 alternative splicing events in 317 patients with BLCA were analyzed, including 4,632 SASEs. The area under the curve of the ROC of risk score (all) was 0.748 for predicting survival status of BLCA patients. Low- and high-risk score groups classified using the median ""risk score (all)"" value displayed remarkably different survival time (Low vs. High = 3304.841±239.758 vs 1198.614±152.460 days). The potential regulatory network with SASEs of splicing factors and other genes was constructed, which might be part of the biological mechanisms associated with prognosis of BLCA patients. CONCLUSIONS: In this study, prognostic signatures constructed using splicing events could be used for predicting the prognosis of BLCA patients."	bladder
Analysis of the association between bladder carcinoma and arsenic concentration in soil and water in southeast Brazil.	In approximately 50% of cases of bladder carcinoma, an associated predisposing factor can be established. The main factors are exposure to tobacco, arsenic (As) ore and aromatic compounds. Arsenic is a metalloid with a low average concentration in the earth's crust, and one of the most dangerous substances for human health. The present study aims to evaluate the incidence of hospitalization and mortality from bladder neoplasia and its possible association with As concentration in water and soil in two of the most critical regions of Brazil: the states of São Paulo and Minas Gerais. We have investigated bladder cancer hospitalization and mortality in the states of São Paulo and Minas Gerais during 2010-2014. Water and soil samples were analyzed and As concentrations were established. Data were obtained through the Department of Informatics of the Brazilian Unified Health System. Correlation was made with water samples from São Paulo and with data on soil analysis from Minas Gerais. The results revealed no direct association in the distinctive municipalities. Areas with high environmental As concentration had a low bladder cancer rate, while areas with normal as levels had similar cancer rates. The quantitative variables did not present a normal distribution (p < 0.05). In conclusion, we did not observe a correlation between as concentration in water or soil and bladder cancer's hospitalization and mortality rates in the states of São Paulo and Minas Gerais.	bladder
Evaluation of glutathione S-transferase pi 1 expression and gene promoter methylation in Moroccan patients with urothelial bladder cancer.	BACKGROUND: Glutathione S-transferase pi 1 (GSTP1) is a cytosolic detoxifying enzyme that protects cells against deleterious effects of oxidative stress. Deregulated expression of GSTP1 protein and aberrant promoter methylation of GSTP1 gene were reported in various human tumors and were shown to be involved in the molecular pathway for cancer development. AIMS AND METHODS: In this study, we aimed to determine the expression status of GSTP1 in relation to its gene promoter methylation in Moroccan population of 30 bladder cancer (BC) patients and in two noncancerous bladder tissues used as controls. GSTP1 expression was assessed by immunohistochemistry and GSTP1 gene promoter methylation status was studied by methylation-specific PCR (MS-PCR). RESULTS: Glutathione S-transferase pi 1 was expressed in the two normal tissues. In BC cases, GSTP1 expression was strong in 23.33% (7/30), moderate in 60% (18/30), and weak in 13.33% (4/30) of cases, while GSTP1 was not expressed in one cancer case (3.33%). Variability of GSTP1 expression does not correlate with high-grade cancer or invasive-stage (p > 0.05). No GSTP1 gene promoter methylation was detected in all control and cancer cases. CONCLUSION: Our data suggest that GSTP1 expression is not associated with BC development, limiting its use as a biomarker for BC management in Morocco. Moreover, difference in GSTP1 expression among BC cases is not due to GSTP1 promoter methylation.	bladder
FGFR3 mutation increases bladder tumourigenesis by suppressing acute inflammation.	Recent studies of muscle-invasive bladder cancer show that FGFR3 mutations are generally found in a luminal papillary tumour subtype that is characterised by better survival than other molecular subtypes. To better understand the role of FGFR3 in invasive bladder cancer, we examined the process of tumour development induced by the tobacco carcinogen OH-BBN in genetically engineered models that express mutationally activated FGFR3 S249C or FGFR3 K644E in the urothelium. Both occurrence and progression of OH-BBN-driven tumours were increased in the presence of an S249C mutation compared to wild-type control mice. Interestingly, at an early tumour initiation stage, the acute inflammatory response in OH-BBN-treated bladders was suppressed in the presence of an S249C mutation. However, at later stages of tumour progression, increased inflammation was observed in S249C tumours, long after the carcinogen administration had ceased. Early-phase neutrophil depletion using an anti-Ly6G monoclonal antibody resulted in an increased neutrophil-to-lymphocyte ratio at later stages of pathogenesis, indicative of enhanced tumour pathogenesis, which supports the hypothesis that suppression of acute inflammation could play a causative role. Statistical analyses of correlation showed that while initial bladder phenotypes in morphology and inflammation were FGFR3-dependent, increased levels of inflammation were associated with tumour progression at the later stage. This study provides a novel insight into the tumour-promoting effect of FGFR3 mutations via regulation of inflammation at the pre-tumour stage in the bladder. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.	bladder
Narrow Band Imaging reduces persistence of cancer in patients with pT1 high grade bladder cancer.	PURPOSE: To evaluate persistence rate on repeated transurethral resection of the bladder (re-TURB) 6 weeks after the first TURB in patients with pT1HG disease undergoing resection of the margins and bed on Narrow Band Imaging. MATERIALS AND METHODS: A consecutive series of patients undergoing TURB and a diagnosis of pT1 high grade disease were prospectively enrolled. On initial TURB patients underwent classic white light resection of the tumour followed by narrow band image (NBI) resection of margins and bed. After 6 weeks from the initial TURB, patients underwent a re-TURB under white light. Persistence rates on re-TURB were recorded. RESULTS: Overall 797 patients underwent TURB, out of them 126 patients with pT1 high grade disease were included in the study. The total number of lesions was 226 meaning 1.79 lesions per patient. On re-TURB 24/126 (19%) of the patients presented residual disease with a total of 28/226 (12%) lesions identified. All these patients presented a pTa residual disease. Out of them 8/21 (38%) presented bladder cancer on the resection bed and 13/21 (62%) presented bladder cancer on margins. CONCLUSION: Narrow Band Imaging trans-urethral resection of the bladder is an oncological effective procedure in the treatment of pT1HG disease. The procedure has a 19% of persistence rate which is inferior when compared to the available evidence on white light TURB. Further multicenter studies are needed in order to validate our results.	bladder
Radiotherapy for High-grade T1 Bladder Cancer.	Radiotherapy is rarely used for T1 bladder cancer. We discuss the potential reasons for this, the current evidence, and make suggestions for future research. PATIENT SUMMARY: Despite its success in muscle-invasive disease, radiotherapy is rarely used for non-muscle-invasive bladder cancer. We discuss the current evidence and suggest that, with further research, radiotherapy holds much promise as a bladder-preserving strategy.	bladder
Validation of Confocal Laser Endomicroscopy Features of Bladder Cancer: The Next Step Towards Real-time Histologic Grading.	BACKGROUND: Cystoscopy enables the visualisation of suspicious bladder lesions but lacks the ability to provide real-time histopathologic information. Confocal laser endomicroscopy (CLE) is a probe-based optical technique that can provide real-time microscopic images. This high-resolution optical imaging technique may enable real-time tumour grading during cystoscopy. OBJECTIVE: To validate and adapt CLE criteria for bladder cancer diagnosis and grading. DESIGN, SETTING, AND PARTICIPANTS: Prospectively, 73 patients scheduled for transurethral resection of bladder tumour(s) were included. CLE imaging was performed intraoperatively prior to en bloc resection. Histopathology was the reference standard for comparison. INTERVENTION: Cystoscopic CLE imaging. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Three independent observers evaluated the CLE images to classify tumours as low- or high-grade urothelial carcinoma (UC), or benign lesions. Interobserver agreement was calculated with Fleiss kappa analysis and diagnostic accuracy with 2×2 tables. RESULTS AND LIMITATIONS: Histopathology of 66 lesions (53 patients) revealed 25 low-grade UCs, 27 high-grade UCs, and 14 benign lesions. For low-grade UC, most common features were papillary configuration (100%), distinct cell borders (81%), presence of fibrovascular stalks (79%), cohesiveness of cells (77%), organised cell pattern (76%), and monomorphic cells (67%). A concordance between CLE-based classification and histopathology was found in 19 cases (76%). For high-grade UC, pleomorphic cells (77%), indistinct cell borders (77%), papillary configuration (67%), and disorganised cell pattern (60%) were the most common features. A concordance with histopathology was found in 19 cases (70%). In benign lesions, the most prevalent features were disorganised cell pattern (57%) and pleomorphic cells (52%), and a concordance with histopathology was found in four cases (29%). CONCLUSIONS: The CLE criteria enable identification of UC. CLE features correlate to histopathologic features that may enable real-time tumour grading. However, flat lesions remain difficult to classify. PATIENT SUMMARY: Confocal laser endomicroscopy may enable real-time cancer differentiation during cystoscopy, which is important for prognosis and disease management.	bladder